bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2025–10–05
thirty papers selected by
Sofia Costa, Matterworks



  1. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2025 Jun 28. pii: 1672-7347(2025)06-1002-11. [Epub ahead of print]50(6): 1002-1012
       OBJECTIVES: Tiletamine, a veterinary anesthetic, has emerged as a novel psychoactive substance and has been abused in many parts of the world, causing great harm to public health. However, the sensitivity of existing detection methods cannot meet the needs of forensic practice. This study aims to establish an ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of tiletamine and its metabolite desethyltiletamine in human biological samples, and to verify its applicability in forensic practice.
    METHODS: SKF525A was used as the internal standard. Biological samples were extracted with acetonitrile containing 1 ng/mL SKF525A, vortexed for 10 min, ultrasonicated for 20 min, centrifuged at 10 000 r/min for 10 min, and 500 μL of the supernatant was filtered through a 0.22 μm membrane. Analyses were performed using an ACQUITY UPLC H-Class PLUS system and an XEVO TQ-S Micro triple quadrupole mass spectrometer. An ACQUITY UPLC® BEH C18 (1.7 µm, 2.1 mm×100 mm) column at a flow rate of 0.3 mL/min was used, and four mobile phase systems were tested to optimize separation. Detection used positive electrospray ionization (ESI+) in multiple reaction monitoring (MRM) mode, with quantifier ion transitions of mass to charge 224.043→179.016 for tiletamine and mass to charge 196.08→151.06 for desethyltiletamine. Calibration curves were established over 0.1-200 ng/mL in spiked blood samples. The linear range, limit of detection (LOD), and limit of quantification (LOQ) were determined. Low (5 ng/mL), medium (20 ng/mL), and high (100 ng/mL) concentrations of tiletamine were spiked into blood, liver, and kidney to evaluate precision, accuracy, matrix effect, recovery, and stability. Finally, actual forensic case samples were tested to validate applicability.
    RESULTS: The established UPLC-MS/MS method achieved simultaneous detection of tiletamine and desethyltiletamine in human biological samples, with retention times of 3.42 min and 2.82 min, respectively. Using mobile phase A (20 mmol/L ammonium acetate and 0.1% formic acid in water) and mobile phase B (acetonitrile) produced the best separation. In blood, tiletamine showed good linearity from 0.1-200 ng/mL (r=0.992, R2=0.983), LOD 0.03 ng/mL, LOQ 0.1 ng/mL, recovery 92%-107%, and matrix effect 71%-99%. In liver and kidney, recoveries were 91%-98% and 93%-104%, and matrix effects were 69%-96% and 72%-100%, respectively. Intra- and inter-day precision [expressed as relative standard deviation (RSD)] and accuracy [expressed as relative error (RE)] were within 15%, and samples were stable at -20 ℃. Tiletamine was detected in actual case samples at 0.37 μg/mL (blood), 0.15 μg/g (liver), 0.11 μg/g (kidney) in case 1, and 8.75 ng/mL (blood) in case 2; desethyltiletamine was also detected in blood.
    CONCLUSIONS: The UPLC-MS/MS method is efficient, accurate, and sensitive, and is suitable for detecting tiletamine and desethyltiletamine in human biological samples.
    Keywords:  biological samples; desethyltiletamine; forensic toxicology; novel psychoactive substances; tiletamine
    DOI:  https://doi.org/10.11817/j.issn.1672-7347.2025.240609
  2. Biomed Chromatogr. 2025 Nov;39(11): e70227
      Tacrolimus is an immunosuppressant commonly used for the prevention of allograft rejection in transplant patients. Liquid chromatography mass spectrometry (LC-MS/MS) method was successfully developed and validated for the estimation of tacrolimus from whole blood. The extraction of the drug was achieved with protein precipitation followed by solid phase extraction. Tacrolimus related compound A was used as an internal standard. Electrospray ionization in negative mode and multiple reaction monitoring were used to monitor the ion transitions. The method was validated for the linear range of 0.200 ng/mL to 50.000 ng/mL with a correlation coefficient > 0.99. The matrix effect due to whole blood matrix was resolved using an optimized time programming coupled with diverter valve (Valco-valve) plumbing. The developed method was used to estimate tacrolimus concentrations from whole blood in a bioequivalence study. The clinical sample analysis was completed without any failure, and the study was found to be bioequivalent.
    Keywords:  Valco‐valve; matrix effect; quality control; specificity; tacrolimus; time programming
    DOI:  https://doi.org/10.1002/bmc.70227
  3. Anal Bioanal Chem. 2025 Sep 29.
      Quantitative mass spectrometry imaging (qMSI) provides information regarding the colocalization, relative abundance, and concentration of a target analyte in a tissue without homogenization. Ionization sources, including IR-MALDESI, commonly utilize an on-tissue spatial calibration curve approach; however, this approach has several limitations including tedious sample preparation, and this approach does not account for local matrix effects. To compensate for these two limitations, we developed voxel-by-voxel (V × V) quantification to provide an internal standard calibration point for every voxel which requires a simple sample preparation and accounts for local matrix effects. In this work, we evaluate the performance of V × V quantification against the spatial calibration curve to assess the quantitative capacity of this newly developed method. Quantification of glutathione (GSH) on a per-voxel basis involves homogenously spraying a known amount of stable isotope-labeled glutathione (SIL-GSH) on a microscope slide. Next, we mount liver sections on top of the coated slides and image them using IR-MALDESI MSI. Statistical analysis demonstrated high precision for V × V quantification over a wide concentration range; however, the method's accuracy is currently limited due to the sprayer's configuration. Results support the feasibility of V × V quantification as evidenced by concentration heatmaps. Additionally, V × V quantification allows for parallel reaction monitoring (PRM) imaging which provides high specificity. Combined with relativity, straightforward sample preparation, and promising initial statistics, the V × V method offers significant advantages over spatial calibration curves.
    Keywords:  IR-MALDESI; Quantitative mass spectrometry imaging; Quantitative sampling; Single-point calibration
    DOI:  https://doi.org/10.1007/s00216-025-06138-x
  4. J Chromatogr A. 2025 Sep 27. pii: S0021-9673(25)00762-9. [Epub ahead of print]1762 466418
      Lipophilic shellfish toxins (LSTs) pose significant health risks through contaminated seafood consumption, necessitating robust monitoring methods, which is critical for early and definitive diagnosis. However, trace analysis of LSTs in human biological fluids remains challenging due to complex matrices and ultra-low concentrations. For this purpose, a rapid, sensitive, and high-throughput UPLC-MS/MS method was developed and validated for the simultaneous determination of 12 LSTs in human plasma, serum, and urine using a μElution 96-well plate for sample preparation. By comparing the extraction efficiency of different types of plate, optimizing dilution factors of eluates, and evaluating matrix effects, a workflow based on the PRiME HLB μElution plate was established for extraction and cleanup, effectively minimizing matrix interference and stabilizing recovery. Chromatographic separation was achieved on a C18 column within 8 minutes using a gradient of water and acetonitrile (both containing 6.7 mmol/L ammonium hydroxide). Target toxins were monitored via multiple reaction monitoring mode with polarity switching (±), and quantified using matrix-matched calibration curves. The method was validated over a linearity of 0.20-30 μg/L (R² > 0.995), with LOQs between 0.03 and 0.77 μg/L. Average recoveries ranged from 69.0 % to 124.0 % with RSDs of 1.1 %-15.3 %. The μElution procedure surpassed conventional SPE in terms of recovery and robustness across all matrices. The method was successfully applied to the analysis of samples from healthy volunteers and LST-dosed rats, detecting two toxins in rat urine. Its simplicity, speed, sensitivity and high-throughput make it a robust tool for LST intoxication detection and biomonitoring.
    Keywords:  Biological fluids; Lipophilic shellfish toxins; Matrix effect; UPLC-MS/MS; μElution extraction
    DOI:  https://doi.org/10.1016/j.chroma.2025.466418
  5. Anal Chim Acta. 2025 Nov 15. pii: S0003-2670(25)00965-1. [Epub ahead of print]1375 344571
       BACKGROUND: Signal intensity drift is a well-recognized issue in quantitative LC-MS(MS) analysis, especially during long analytical sequences or when internal standards (IS) are unavailable. While IS correction is widely supported by commercial platforms, other correction strategies, such as quality control (QC)-based drift correction, or quantification bracketing, are unavailable. This limits the ability of analysts to maintain data quality in more complex or resource-limited experimental setups. To address this, we developed QuantyFey, an open-source, vendor-independent tool for external calibration-based quantification, with support for multiple drift correction strategies.
    RESULTS: We applied QuantyFey to a targeted LC-MS/MS dataset comprising amino acids, amino acid-related metabolites, and biogenic amines measured in porcine plasma. The dataset was affected by substantial signal drift across the run. A calibration standard was used as a proxy for a QC sample and different drift correction strategies were compared: IS correction, QC-based drift correction, custom bracketing and weighted bracketing. Concentrations of all compounds were calculated using different drift correction strategies and manual tuning of calibration functions, and remaining intensity drift was assessed. Both QC-based and IS-based correction significantly reduced drift effects. Custom- or weighted bracketing methods also improved quantification accuracy but demonstrated variable performance across compounds. This study highlights the importance of evaluating compound-specific behavior when selecting drift correction strategies.
    SIGNIFICANCE: QuantyFey offers a transparent and accessible framework for quantitative LC-MS(MS) analysis, especially in situations where drift correction is critical and IS are limited. Its flexible design allows for compound-specific evaluation and quantification, making it a practical tool for handling complex datasets. By supporting tailored drift correction strategies, QuantyFey addresses key challenges in maintaining data quality and reproducibility.
    Keywords:  Intensity-drift; LC-MS; R; Shiny; Tandem mass spectrometry; Targeted metabolomics
    DOI:  https://doi.org/10.1016/j.aca.2025.344571
  6. Methods Mol Biol. 2026 ;2697 137-152
      Quantitative metabolomics is based on a set of experimental approaches to accurately quantify intracellular metabolite concentrations. This allows us to characterize the response of a metabolic network (i.e., the metabolic phenotype) to an environmental or genetic perturbation. Here, we describe a four-step protocol adapted to the methylotrophic yeast Komagataella phaffii: (1) separation of the cells from the fermentation broth by cold filtration and addition of 13C-labeled cell extract, (2) a metabolic quenching step based on aqueous cold methanol, (3) a metabolite extraction method based on boiling ethanol, and (4) quantification by isotope dilution mass spectrometry (LC-IDMS/MS and/or GC-IDMS). This method allows us to quantify most metabolites of central carbon metabolism, including glycolytic, tricarboxylic acid cycle, and pentose phosphate pathway intermediates, as well as cofactors and free amino acids. This method has been validated for K. phaffii grown on glucose, as well as on a mixture of carbon substrates such as methanol in combination with glucose or glycerol.
    Keywords:  13C-labeled internal standard; Extraction; Intracellular metabolites; Isotope dilution mass spectrometry; Komagataella phaffii; Metabolomics; Microbial metabolism; Pichia pastoris; Quenching
    DOI:  https://doi.org/10.1007/978-1-0716-4779-0_8
  7. Eur J Mass Spectrom (Chichester). 2025 Oct 03. 14690667251384047
      Naltrexone, an FDA-approved mu-opioid receptor antagonist for alcohol dependence, requires therapeutic drug monitoring due to its pharmacokinetic variability. This study developed a liquid chromatography-electrospray ionization-tandem mass spectrometry method for accurately quantifying naltrexone and its active metabolite, 6β-naltrexol, using deuterated internal standards (naltrexone-d3 and 6β-naltrexol-d3). Sample preparation involved solid-phase extraction with a Strata-X cartridge followed by elution. Separation was performed on a C18 column with gradient elution at 0.3 mL/min. Detection in dynamic multiple reaction monitoring mode used ion transitions at m/z 342 > 324 for naltrexone and m/z 344 > 161 for 6β-naltrexol. The calibration curves were linear over the range of 0.0152-33.3 ng/mL for naltrexone and 0.410-100. ng/mL for 6β-naltrexol, both with a correlation coefficient of 1.0000 and 0.9998, individually. Intraday and interday variations were below 9.2% for naltrexone and 6.6% for 6β-naltrexol. The recovery was 99.5% for naltrexone and 95.0% for 6β-naltrexol. Applied to plasma samples from five patients receiving 50 mg oral naltrexone daily for 12 weeks, average concentrations were 3.30 ± 4.40 ng/mL (naltrexone) and 48.5 ± 23.4 ng/mL (6β-naltrexol). The developed assay method effectively quantifies naltrexone and its metabolite in alcohol-dependent patients in Taiwan.
    Keywords:  6β-naltrexol; LC-MS/MS; alcohol use disorder; naltrexone; therapeutic drug monitoring
    DOI:  https://doi.org/10.1177/14690667251384047
  8. J Pharmacol Toxicol Methods. 2025 Sep 25. pii: S1056-8719(25)00820-2. [Epub ahead of print]136 108400
      A highly sensitive and reproducible liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was systematically developed and optimized using a Quality by Design (QbD) framework for the simultaneous quantification of chlorthalidone and cilnidipine in rat plasma. Critical method variables-organic phase composition, flow rate, and mobile phase pH-were identified through risk assessment and subsequently optimized via Box-Behnken Design to ensure analytical robustness. Optimal chromatographic conditions comprised 20 % organic content, a flow rate of 1.0 mL/min, and a mobile phase pH of 3.0, facilitating efficient resolution of both analytes. Detection was achieved in positive electrospray ionization mode using multiple reaction monitoring, with transitions of m/z 339.8909 → 85.0951 for chlorthalidone, m/z 493.5237 → 300.1587 for cilnidipine, and m/z 515.6423 → 342.6158 for telmisartan, employed as the internal standard. Method validation, performed in accordance with European Medicines Agency (EMA) guidelines, demonstrated excellent linearity (r2 > 0.998), accuracy, and precision, with coefficient of variation consistently <10 %. The method exhibited strong analyte stability and was successfully applied to the pharmacokinetic evaluation of both drugs in Wistar rats. This DoE-optimized LC-MS/MS platform offers a selective, reliable, and environmentally conscious analytical solution for the preclinical assessment of chlorthalidone and cilnidipine.
    Keywords:  Chlorthalidone; Cilnidipine; Design of Expert; Green analytical chemistry; LC-MS/MS; Pharmacokinetic
    DOI:  https://doi.org/10.1016/j.vascn.2025.108400
  9. Ther Drug Monit. 2025 Oct 02.
       BACKGROUND: The endocannabinoid system regulates immune function, inflammation, and metabolism and has gained increasing attention in clinical research. However, the instability, low abundance, and physicochemical complexity of endocannabinoids (ECs) and EC-like substances (EC-like) make their quantification in plasma analytically challenging.
    OBJECTIVE AND METHODS: The authors developed and validated a liquid chromatography-tandem mass spectrometry method for the simultaneous quantification of N-arachidonoylethanolamide (AEA), 2-arachidonoylglycerol, and its isomer 1-arachidonoylglycerol (2-AG/1-AG), oleoylethanolamide (OEA), and palmitoylethanolamide (PEA) in human plasma.
    RESULTS: Extraction was performed using liquid-liquid extraction combined with liquid chromatography-tandem mass spectrometry. The method achieved lower limits of quantification of 0.1 mcg/L for AEA, 0.2 mcg/L for 2-AG/1-AG, and 0.5 mcg/L for OEA and PEA, with calibration curves showing high linearity (R2 ≥ 0.995). Intra-assay and interassay accuracy and precision were both within 15%. Additional validation parameters, including selectivity, recovery, carryover, matrix suitability, and dilution integrity, fulfilled regulatory criteria. Preanalytical handling significantly influenced concentrations: Delayed centrifugation and postthaw storage increased AEA, OEA, and PEA levels. The validated method was applied to plasma samples from patients coinfected with HIV and hepatitis C virus, enabling reproducible quantification of ECs and EC-like substances in a clinically relevant cohort.
    CONCLUSIONS: The study demonstrates that biological and technical factors markedly affect plasma EC and EC-like concentrations. Standardized preanalytical processing is therefore essential for accurate measurement, and the proposed method provides a robust tool for clinical and pharmacological research.
    Keywords:  HIV-HCV co-infection; LC-MS/MS; endocannabinoids
    DOI:  https://doi.org/10.1097/FTD.0000000000001397
  10. J Mass Spectrom. 2025 Oct;60(10): e5184
      Mass calibration techniques are vital in achieving high mass measurement accuracy (MMA) of large biomolecules. Variable ion populations that shift the axial frequencies due to space charge effects have been a significant challenge in achieving sub-parts-per-million (sub-ppm) MMA of glycans on a high-resolution accurate mass (HRAM) orbitrap instrument without the activation of automatic gain control. As the role of glycans is critical to our understanding of diverse biological processes, accurate identification of glycans using sub-ppm MMA is critical for biological interpretations. Hence, this study aims to achieve sub-ppm MMA of glycans by exploring the impact of different ion accumulation times, data collection modes, in addition to custom calibration strategies and external mass correction to optimize accurate mass measurements. Using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI), direct analysis was performed on N-linked glycans cleaved from bovine fetuin in negative polarity, where 17 N-linked glycans were detected and annotated. Our results indicate the significance of implementing a custom calibration external lock mass and other techniques, including the effect of external mass correction in achieving sub-ppm MMA of large biomolecules. Implementing such approaches in mass spectrometry imaging (MSI) of biological tissue will enhance the confidence of glycan annotation and enable more accurate biological conclusions.
    Keywords:  IR‐MALDESI; N‐linked glycans; custom calibration; mass calibration; mass measurement accuracy
    DOI:  https://doi.org/10.1002/jms.5184
  11. Anal Methods. 2025 Oct 01.
      Alvocidib, an approved drug for the treatment of acute myeloid leukemia, undergoes glucuronidation metabolism. The purpose of this study is to develop a robust and sensitive LC-MS/MS method to simultaneously quantify alvocidib and its metabolite, alvocidib-glucuronide (Alv-G), and apply this method in a pharmacokinetic and tissue distribution study in rats. A UHPLC system coupled to an AB Sciex QTrap 4000 triple quadrupole mass spectrometer was used for the analysis. The analytes were separated using a Biphenyl column with 0.1% formic acid in water and acetonitrile as the mobile phases and were quantified under positive electrospray ionization (ESI) mode using a multiple reaction monitoring (MRM) approach. Protein precipitation with acetonitrile was used in sample processing. The method showed a good linearity within the range of 2.4-5000.00 nM for both analytes. The method was reproducible, with intra and inter-day accuracy and precision ranging from 84-98% and <13% respectively. The extraction recovery and matrix effect achieved acceptable ranges (82-105%). Stability studies demonstrated that they were stable under bench-top (91-99%), freeze-thaw (83-110%), and long-term storage conditions (80-106%). The PK results showed that after oral administration of alvocidib, both alvocidib and Alv-G were detected in plasma with the parent drug showing highest distribution in the colon, and lowest in the small intestine. In contrast, Alv-G showed the highest distribution in the small intestine and the lowest amount in the colon compared to the other tissues. This method is applicable for PK and tissue distribution studies to quantify both alvocidib and its glucuronide.
    DOI:  https://doi.org/10.1039/d5ay01143d
  12. Anal Bioanal Chem. 2025 Oct 02.
      The analysis of sterol biosynthesis poses analytical challenges such as vast concentration differences between precursor molecules and cholesterol as well as the substantial interferences between the sterols and the matrix, resulting in strong ion suppression. LC-MS and 2D-LC-MS may address some of these challenges, but for sensitive and robust detection, ionization plays a key role. Electrospray ionization (ESI) stands out for its capability to generate ions from polar and nonpolar compounds, rendering it suitable for a broad spectrum of analytes, including sterols. Atmospheric pressure chemical ionization (APCI) demonstrates efficacy for compounds exhibiting moderate to low polarity, thereby facilitating efficient ionization of sterols. Tube plasma ionization (TPI) is a relatively new technique that promises sensitive ionization across a wide polarity range, indicating its potential utility for sterol analysis. Here, a new tube plasma ion source for LC-MS was developed and compared with established ion sources (ESI and APCI) for sterol analysis. The TPI source showed comparable LOQs to APCI and clearly outperformed ESI in terms of sensitivity. Both TPI and APCI provided stable signals during extended measurement series, while ESI suffered from pronounced ion suppression. Application to human plasma, HepG2 cells, and liver tissue demonstrated that TPI provided results in close agreement with APCI, highlighting its robustness for sterol quantification in complex biological matrices.
    Keywords:  Atmospheric pressure ionization; Heart-cutting 2D-LC; Ion suppression; Liquid chromatography ion sources; Tube plasma ionization
    DOI:  https://doi.org/10.1007/s00216-025-06126-1
  13. Ther Drug Monit. 2025 Sep 30.
       BACKGROUND: The dexamethasone suppression test (DST) is a key diagnostic tool for evaluating disorders of the hypothalamic-pituitary-adrenal (HPA) axis. Interpretation of DST results can be confounded by inadequate dexamethasone exposure due to pharmacokinetic variability or patient nonadherence. Simultaneous measurement of dexamethasone and cortisol by LC-MS/MS improves diagnostic accuracy by distinguishing true biological nonsuppression from insufficient drug exposure and prevents analytical interferences observed with cortisol immunoassays.
    METHODS: A commercially available CE-IVD LC-MS/MS steroid panel (Chromsystems) was adapted for the simultaneous quantification of dexamethasone and cortisol in human plasma. The method was validated for linearity, accuracy, precision, selectivity, carry-over, matrix effects, and stability. Method comparison was performed using 26 clinical DST samples analyzed using immunoassay and external LC-MS testing. The proposed dexamethasone cutoff of 1.3 ng/mL (3.3 nmol/L) was evaluated in 62 patient samples.
    RESULTS: The method demonstrated excellent linearity, with intra- and interassay accuracy and precision within ±15% for both analytes. No relevant carry-over or matrix effects were observed. Agreement with reference methods was 91% ± 6% for cortisol and 95% ± 7% for dexamethasone. Among the 62 DST samples, 48 showed appropriate suppression [cortisol <18.12 ng/mL (<50 nmol/L)] with dexamethasone levels above the cutoff. In contrast, 3 samples with insufficient suppression [cortisol >48.6 ng/mL (134.1 nmol/L)] had subthreshold dexamethasone levels, whereas 11 samples showed elevated cortisol levels despite sufficient dexamethasone exposure, indicating possible HPA axis dysfunction.
    CONCLUSIONS: The proposed rapid and robust LC-MS/MS method enables reliable, simultaneous quantification of dexamethasone and cortisol. The assay supports accurate DST interpretation by identifying cases of pharmacokinetic variance or nonadherence.
    Keywords:  Cushing syndrome; LC-MS/MS; cortisol; dexamethasone; steroids
    DOI:  https://doi.org/10.1097/FTD.0000000000001389
  14. J Sep Sci. 2025 Oct;48(10): e70274
      Structurally similar oxysterols such as 7α-hydroxycholesterol, 7β-hydroxycholesterol, and 7-ketocholesterol; 5,6α- and 5,6β-epoxycholesterol; and 24(R/S)-hydroxy cholesterol, 25-hydroxy cholesterol, and 27-hydroxycholesterol are traditionally difficult to resolve using reversed-phase liquid chromatography (RPLC). We present a simple yet highly optimized method for the simultaneous quantification of eight oxysterols using RPLC coupled with mass spectrometry (MS) without derivatization. Optimal separation of most oxysterols was achieved at a lower column temperature (25°C), with specific combinations of stationary and mobile phases enhancing resolution, particularly for isomeric pairs such as 7α-/7β-OHC, 5,6α-/5,6β-EC, 24 R/S-OHC, and 25-OHC. Although certain analytes (e.g., 24S-OHC and 27-OHC) remained challenging to separate due to similar retention behavior, they were distinguishable by their unique MRM transitions. We applied this method to investigate oxysterol changes in a longitudinal mouse study comparing a normal diet to a high-fat diet. Liver and brain samples were analyzed, revealing distinct distribution patterns between the two organs. Notably, 24(S)-hydroxycholesterol levels, a signature cholesterol metabolite exclusively produced in the brain, increased with age independent of diet. In contrast, 5,6α-epoxycholesterol production in the liver was influenced by both age and dietary factors. Our method provides a robust tool for studying oxysterol variation and its implications in aging and diet, offering new insights into cholesterol-derived lipid regulation across different physiological conditions.
    DOI:  https://doi.org/10.1002/jssc.70274
  15. J Anal Methods Chem. 2025 ;2025 8995925
      This study developed a method for simultaneously detecting 10 mycotoxins in Dendrobium officinale using the QuEChERS technique combined with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The method was optimized for sample purification, pretreatment, chromatographic conditions, and mass spectrometric settings. It effectively addressed the matrix effects from impurities like pigments and cellulose. The validation of the method showed good linearity (R 2 > 0.990), with limits of detection (LODs) ranging from 0.23 to 8.61 μg kg-1 and limits of quantification (LOQs) from 0.77 to 28.7 μg kg-1. Average recoveries for the 10 mycotoxins ranged from 77.9% to 98.5%, with relative standard deviations (RSD) between 2.26% and 8.28%. The method demonstrated high accuracy, precision, and suitability for large-scale screening of mycotoxins in Dendrobium officinale. When applied to 84 samples, the contamination rate was 2.38%, with the main contaminants being AFB1, ZEN, and AFG1. This method provides a reliable, cost-effective approach for detecting mycotoxin contamination in traditional Chinese medicine.
    Keywords:  QuEChERS; UHPLC–MS/MS; dendrobium officinale; matrix effect; mycotoxins; sample purification
    DOI:  https://doi.org/10.1155/jamc/8995925
  16. Forensic Toxicol. 2025 Oct 02.
       PURPOSE: The abuse of 2-fluoro-2-oxo-phenylcyclohexylethylamine (2F-2-oxo-PCE), a dissociative anesthetic structurally related to phencyclidine (PCP) and ketamine, has recently increased in South Korea. This study presented the first forensic toxicological detection of 2F-2-oxo-PCE in autopsy cases and described a validated method for the simultaneous quantification of 2F-2-oxo-PCE, methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA), ketamine, and norketamine in postmortem blood.
    METHOD: 2F-2-oxo-PCE and its metabolite, 2F-deschloronorketamine (2F-DCNK) were identified using gas chromatography-mass spectrometry (GC-MS). A liquid chromatography-tandem mass spectrometry (LC-MS/MS) with solid-phase extraction (SPE) was developed and validated for the simultaneous quantification of 2F-2-oxo-PCE, MDMA, MDA, ketamine and norketamine in blood.
    RESULTS: The validation parameters including linearity, accuracy, precision, matrix effect, and recovery were satisfactory. In postmortem blood samples, 2F-2-oxo-PCE concentrations ranged from 664 to 7911 ng/mL. Concurrent detection with MDMA and ketamine suggested possible polydrug use contributing to fatal outcomes.
    CONCLUSIONS: The validated LC-MS/MS method is suitable for forensic applications and may enhance the toxicological profiling of emerging dissociative substances. The results can provide critical baseline data for interpreting 2F-2-oxo-PCE-related intoxications.
    Keywords:  2F-2-oxo-PCE; Ketamine; LC-MS/MS; MDMA; Postmortem
    DOI:  https://doi.org/10.1007/s11419-025-00743-2
  17. Talanta. 2025 Sep 30. pii: S0039-9140(25)01410-9. [Epub ahead of print]298(Pt A): 128919
      Acetoacetate (AcAc) and β-hydroxybutyrate (βOHB) are ketone bodies involved in energy metabolism, particularly during physiological states of glucose scarcity, such as fasting, exercise, and the implementation of a ketogenic diet. The production (ketogenesis) and utilization (ketolysis) of ketone bodies are dynamic processes that can be quantified using stable isotope-labeled tracers in metabolic tracing studies, necessitating precise and sensitive analytical methods for accurately measuring both labeled and unlabeled pools. Although UHPLC-MS/MS has recently emerged as a reliable tool for quantifying ketone bodies, its dependence on 13C-labeled internal standards limits its utility in 13C-based tracer studies. AcAc, in particular, poses challenges due to its chemical instability and the scarcity of authentic, stable, isotopically labeled internal standards. While the chemical reduction of AcAc to βOHB provides a solution, this necessitates a cumbersome desalting step. To overcome these limitations, we developed a novel approach using deuterated AcAc (d3-AcAc) and [3,4,4,4-d4]βOHB as internal standards for the simultaneous quantification of 13C-labeled and unlabeled ketone bodies in biological samples. We optimized the synthesis of AcAc from ethyl-AcAc via base-catalyzed hydrolysis, achieving 99.2 ± 0.2 % purity at 60 °C for 3 h, as confirmed by 1H NMR. Stability assessments in the extraction buffer and post-extraction serum samples confirmed the robustness of newly synthesized d3-AcAc for at least 5 h. A comparative analysis against the labor-intensive conventional method demonstrated superior precision, accuracy, and ease of application, enabling high-throughput metabolic and clinical studies. The optimized UHPLC-MS/MS method substantially improves metabolic tracing capabilities, enabling rapid and accurate investigation of ketone body tracing studies across various physiological and pathological conditions.
    Keywords:  Acetoacetate; Beta-hydroxybutyrate; Flux modeling; Ketone bodies; Quantification; Stable isotopes
    DOI:  https://doi.org/10.1016/j.talanta.2025.128919
  18. Methods Mol Biol. 2026 ;2975 135-150
      With the increasing number of dystrophin replacement therapy trials, the need for reliable and accurate dystrophin quantification in muscle biopsies is becoming an important outcome measure. Quantification of dystrophin protein by mass spectrometry provides advantages over methods such as western blotting by offering improved precision, reproducibility, specificity, and a large quantifiable dynamic range. This protocol details a targeted mass spectrometry method for quantifying dystrophin in total muscle protein extracts using stable isotope-labeled dystrophin as a spike-in standard.
    Keywords:  DMD; Dystrophin; In-gel digestion; Parallel reaction monitoring; Quantification; SDS-PAGE; SILAC; Targeted mass spectrometry
    DOI:  https://doi.org/10.1007/978-1-0716-4811-7_9
  19. Anal Chem. 2025 Oct 03.
      The ability to characterize closely related lipids is clinically important, requiring the development of analytical tools to differentiate species responsible for metabolic disorders from those needed for metabolic homeostasis. Herein, we report a new liquid chromatographic (LC) method that utilizes online microdroplet-based epoxidation reactions during electrospray to enable C═C bond localization on conventional tandem mass spectrometry (MS/MS). Through a coaxial spray mechanism, charged microdroplets derived from the LC column and containing the lipid analyte were fused with nonthermal plasma, which facilitated (i) positive ion mode detection of various lipid classes and (ii) instantaneous C═C bond epoxidation via reaction with reactive oxygen species in the nonthermal plasma. Consequently, conventional low-energy MS/MS based on collision-induced dissociation was effective in characterizing the positional isomers of various lipids. Our ability to modify electrosprayed microdroplets post-column allowed independent optimization of the LC mobile phase, which in turn enabled both polar and nonpolar lipids to be separated on a C12 reverse-phase column. A data-dependent acquisition (DDA) method was created to enable the automated characterization of epoxide products in a 17-component lipid mixture. The DDA method was applied to characterize new triacylglycerol previously not detected in extra virgin olive oil.
    DOI:  https://doi.org/10.1021/acs.analchem.5c02269
  20. Environ Sci Technol. 2025 Sep 30.
      Detecting PFAS is challenging due to their diverse chemical structures, lack of standards, complex sample matrices, and the need for sensitive equipment to measure trace levels. Background contamination and the sheer number of PFAS further hinder the development of a universal detection method. Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is the primary tool capable of analyzing PFAS in water, soil, and biological samples, and it is widely adopted in regulatory testing. However, LC-HRMS faces challenges, including contamination risk, labor-intensive preparation, low detection limits, and time-consuming data processing that requires advanced software and expertise to distinguish structurally similar compounds. To overcome these obstacles, we present DeePFAS, a deep-learning-based method for rapid annotation of PFAS. DeePFAS employs a spectral encoder integrating convolutional and transformer architectures to project raw MS2 spectra into a latent space of chemical structural features learned from a large corpus of unlabeled compounds. DeePFAS enables efficient annotation of MS2 spectra by comparing latent representations with candidate molecules, streamlining large-scale nontargeted PFAS screening, and reducing analytical complexity. Our method demonstrates the potential of AI-driven tools in environmental chemistry and is available at https://github.com/CMDM-Lab/DeePFAS.
    Keywords:  PFAS (per- and polyfluoroalkyl substances); chemically latent space; deep learning; environmental analysis; mass spectrometry
    DOI:  https://doi.org/10.1021/acs.est.5c09769
  21. J Pharm Biomed Anal. 2025 Sep 30. pii: S0731-7085(25)00518-7. [Epub ahead of print]267 117177
      Nucleosides and their modified forms serve as fundamental building blocks of nucleic acids and play critical roles in epigenetic regulation, RNA metabolism, and cellular signaling. In this study, we developed and validated a rapid, sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous quantification of 27 endogenous nucleosides-including 12 canonical nucleosides, 11 modified nucleosides, and 4 mononucleotides-in cellular samples. Under optimized chromatographic conditions, good separations and peak shapes for 27 target compounds were achieved within a 13.0-min gradient elution. The overall LOQs were between 0.2 and 25.0 ng/mL. The intra-day precision of the method was less than 8.2 %, and the inter-day precision was less than 14.2 %. The accuracy was in the range of 89.9-112.2 % for all analytes. The developed method was successfully applied to analyze the metabolic profiles of gastric cancer cells with varying differentiation degrees (NCI-N87, SGC-7901, MGC-803). The results revealed distinct nucleotide metabolism alterations linked to tumor progression and identified potential biomarkers for gastric cancer advancement.
    Keywords:  Gastric cancer; Method development; Modified nucleosides; Nucleotide metabolism; UHPLC-MS/MS
    DOI:  https://doi.org/10.1016/j.jpba.2025.117177
  22. Talanta. 2025 Sep 28. pii: S0039-9140(25)01409-2. [Epub ahead of print]298(Pt A): 128918
      The study of drug metabolites is essential for evaluating safety and optimizing drug design. Recent classes of high-molecular-weight drugs, such as PROTACs and LYTACs, present challenges for traditional metabolite identification approaches due to their complex structures. To address these limitations, we developed Drug Metabolite Finder (DMetFinder), a novel mass spectrometry-based tool designed to enhance metabolite identification. DMetFinder employs cosine similarity algorithms to filter compounds with similar structures, minimizing the risk of overlooking metabolites with large fragment losses. It also efficiently detects multiply charged ions and incorporates isotope abundance and adduct ion scoring to refine identification accuracy. By calculating a total weighted score, DMetFinder reduces false positives associated with single-filter strategies. Experimental validation demonstrates that DMetFinder significantly improves the identification of metabolites from PROTACs, providing valuable insights for future drug development.
    Keywords:  DMetFinder; Drug metabolites; Isotope pattern; LC-MS/MS; Mass defect filter; Spectrum similarity
    DOI:  https://doi.org/10.1016/j.talanta.2025.128918
  23. Environ Sci Technol. 2025 Sep 30.
      Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) enables profiling of hundreds of externally derived chemicals and their metabolites in human biofluids to capture the internal chemical exposome. Nevertheless, developing sensitive and robust high-throughput methodologies to scale up exposomics remains challenging. We compared two validated sample preparation methods (SPMs) based on protein precipitation (PPT) and PPT combined with phospholipid removal (PLR) in two cohorts using blood plasma (n = 109) and serum (n = 75) to assess their impact on LC-HRMS repeatability and chemical coverage. Additional filtration on PLR plates allowed the injection of extracts twice concentrated without affecting LC-HRMS repeatability. The comparison of chemical coverage between SPMs was then assessed using 184 compounds (including a large variety of exogenous chemicals) annotated with a suspect screening strategy. Most chemicals (78-86%) were detected with both SPMs, but a substantial fraction showed preferential (>2-fold, 37-50%) or exclusive (14-22%) detection with one SPM, reflecting differences in matrix effects and/or recoveries. Low-abundance chemicals were more sensitive to the choice of SPM, though no predictive trends related to physicochemical properties emerged, likely due to higher analytical uncertainty. Overall, both SPMs provided acceptable chemical coverage for large-scale exposomics. Nonetheless, the compound-dependent nature of detection highlights the value of applying complementary SPMs when feasible.
    Keywords:  LC–HRMS; exposomics; human blood; phospholipid removal; protein precipitation; sample preparation
    DOI:  https://doi.org/10.1021/acs.est.5c01686
  24. J Sep Sci. 2025 Oct;48(10): e70279
      Routine monitoring of vancomycin drug concentrations is crucial for optimizing dosages to ensure therapeutic efficacy and minimize adverse effects. Vancomycin's clearance is highly correlated with creatinine clearance. However, in developing countries, the majority of hospitals lack the on-site capacity to measure vancomycin concentrations. Dried plasma spots have emerged as an innovative alternative for biological sample collection. Dried plasma spots facilitate the convenient and rapid acquisition of plasma samples, which are highly suitable for both storage and transportation, and can be dispatched to vancomycin testing laboratories. This study presents a validated methodology for the simultaneous quantification of vancomycin and creatinine in dried plasma spots through liquid chromatography-tandem mass spectrometry. Vancomycin demonstrated excellent linearity within the range 3-50 µg/mL, while creatinine exhibited linearity from 1 to 70 µg/mL (both with r2 > 0.995). The trueness of all compounds was maintained within ± 15%, the precision was less than 15%, and the recoveries were within acceptable boundaries. Moreover, no significant matrix effects were detected. By employing the Passing-Bablok and Bland-Altman methods, we compared the differences and consistencies between the wet plasma concentrations and dried plasma spot concentrations of vancomycin and creatinine in 71 samples. The results revealed no significant distinctions between the two approaches and showcased comparable consistencies, implying that the dried plasma spots technique can be effectively utilized for the simultaneous determination of vancomycin and creatinine in plasma.
    Keywords:  creatinine; dried plasma spot; liquid chromatography‐tandem mass spectrometry; therapeutic drug monitoring; vancomycin
    DOI:  https://doi.org/10.1002/jssc.70279
  25. J Proteome Res. 2025 Oct 02.
      Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.
    Keywords:  data formats; lipidomics; mass spectrometry; metabolomics; proteomics; proteomics standards initiative; standards
    DOI:  https://doi.org/10.1021/acs.jproteome.5c00435
  26. Nat Commun. 2025 Sep 30. 16(1): 8714
      Mass spectrometry-based lipidomics and metabolomics generate extensive data sets that, along with metadata such as clinical parameters, require specific data exploration skills to identify and visualize statistically significant trends and biologically relevant differences. Besides tailored methods developed by individual labs, a solid core of freely accessible tools exists for exploratory data analysis and visualization, which we have compiled here, including preparation of descriptive statistics, annotated box plots, hypothesis testing, volcano plots, lipid maps and fatty acyl chain plots, unsupervised and supervised dimensionality reduction, dendrograms, and heat maps. This review is intended for those who would like to develop their skills in data analysis and visualization using freely available R or Python solutions. Beginners are guided through a selection of R and Python libraries for producing publication-ready graphics without being overwhelmed by the code complexity. This manuscript, along with associated GitBook code repository containing step-by-step instructions, offers readers a comprehensive guide, encouraging the application of R and Python for robust and reproducible chemometric analysis of omics data.
    DOI:  https://doi.org/10.1038/s41467-025-63751-1
  27. Rapid Commun Mass Spectrom. 2026 Jan;40(1): e10142
       RATIONALE: Direct metabolic analysis is crucial for understanding the mechanisms of various diseases. However, it is still difficult to perform direct metabolic analysis of native biofluids for many biological sample types because conventional workflows often necessitate extensive sample pretreatment to mitigate matrix interference from high salt concentrations.
    METHODS: In this study, we developed a novel approach using a Wimshurst Machine-nanoelectrospray ionization (WM-nanoESI) system for direct metabolic analysis of native biofluids. This device achieves direct metabolic analysis due to its sampling method (injecting biofluid directly into nanoESI emitters with an orifice diameter of approximately 10 μm) and the adaptive electricity provided by the Wimshurst machine (preventing tip clogging and extending duration time).
    RESULTS: This method enables qualitative analysis of drugs and metabolites, prevents tip clogging when analyzing PBS and serum, and extends the duration time by approximately 15-fold longer than traditional DC nanoESI does. HeLa and MCF-7 cells were distinguished according to their metabolic profiles.
    CONCLUSIONS: Our results indicate that the WM-nanoESI will offer significant advancements for real-time metabolic monitoring, boost disease understanding, and therapeutic monitoring.
    Keywords:  biofluids; direct; metabolic; nanoelectrospray ionization
    DOI:  https://doi.org/10.1002/rcm.10142
  28. Drug Des Devel Ther. 2025 ;19 8679-8689
       Propose: A bromodomain and extra-terminal domain inhibitor (I-BET151) is effective in treating chronic graft-versus-host disease and has been extensively studied in recent years. However, there is limited research on the pharmacokinetics of I-BET151, especially the lack of methods for determining the concentration of I-BET151 in vivo. Therefore, the purpose of this study is to establish an HPLC-MS/MS method for determining the plasma concentration of I-BET151 and use it for pharmacokinetic study in rats.
    Methods: The chromatographic column is a Poroshell 120EC-C18 column (50 mm × 4.6 mm, 2.7 μm). The mobile phase consists of water containing 20 mmol ammonium acetate and 0.1% formic acid, and methanol containing 0.1% formic acid, with a flow rate of 0.6 mL/min. The extraction of I-BET151 is liquid-liquid extraction, and the extraction solvent is ether:dichloromethane=2:3. The HPLC-MS/MS method was validated based on the guidelines of quantitative methods for biological samples in the Chinese Pharmacopoeia, including specificity, standard curve, lower limit of quantification, residual effects, precision, recovery rate, matrix effects, stability, etc.
    Results: The results showed that the established method met the requirements of methodological validation standards and could be used for pharmacokinetic studies of I-BET151. The pharmacokinetic results displayed that the half-life of oral and intravenous administration of I-BET151 was 4.3 h and 3.1 h, respectively. The oral bioavailability was about 60%, indicating that I-BET151 had a high oral bioavailability and appropriate half-life, demonstrating good clinical application prospects.
    Keywords:  HPLC-MS/MS; I-BET151; bioavailability; method validation; pharmacokinetics
    DOI:  https://doi.org/10.2147/DDDT.S540415
  29. Anal Bioanal Chem. 2025 Oct 04.
      Sample preparation, particularly lipid extraction, plays a critical role in lipidomics workflows and strongly influences analytical outcomes. In biomedical research, the most commonly used lipid extraction protocols rely on chloroform due to its favorable physicochemical properties, including the ability to dissolve both polar and apolar lipids, as well as its high volatility. Although well-established chloroform-based methods enable high recovery of a broad range of lipids, concerns about the toxicity and environmental impact of chloroform necessitate the development of more sustainable alternatives. In this study, a combined computational and experimental strategy was employed to identify and validate greener solvents suitable for lipid extraction in lipidomics applications. Solvent selection was guided by Hansen solubility parameters, Abraham solvation descriptors, and principal component analysis, yielding five candidate solvents as potential chloroform alternatives. Evaluation of solvent sustainability and human health risk was conducted using CHEM21 criteria and supplemented by a comprehensive literature review. Initial validation of extraction efficiency for identified candidates was performed using synthetic lipid standards in the absence of a biological matrix, followed by testing lipid extraction from human plasma using both monophasic and biphasic extraction protocols. The highest extraction efficiency was achieved using a single-phase extraction method based on cyclopentyl methyl ether, which exhibited comparable and even superior performance to the conventional chloroform-based Folch protocol. Overall, this study highlights the feasibility of replacing chloroform with less hazardous solvents in lipidomics workflows without compromising analytical performance, and provides a comparative assessment of computational solvent prediction approaches for green chemistry applications.
    Keywords:  Chloroform alternatives; Green solvents; Lipid extraction; Lipidomics; Modelling
    DOI:  https://doi.org/10.1007/s00216-025-06136-z
  30. Methods Mol Biol. 2026 ;2963 79-89
      Altered phospholipid compositions in skeletal muscle occur in muscular dystrophy and other pathological conditions; however, origins and relationships to the disease course are unclear. Liquid chromatography-mass spectrometry (LC-MS) technologies allow the determination of phospholipid compositions and alteration patterns in disease states. Here, we describe a basic protocol to prepare methanolic extracts from skeletal muscle, which may be analyzed by lipidomic LC-MS in order to detect compositional alterations in phosphatidylcholine, a major phospholipid species of skeletal muscle, as well as other phospholipid classes such as phosphatidylethanolamine. These analyses are useful to determine relative increases or decreases in individual phospholipid species between samples and capture changes in membrane compositions rather than the absolute quantities of lipids. LC-MS lipidomic analyses often yield large datasets containing hundreds of chromatographic peaks for each sample, and a ratiometric analysis strategy to determine the relative abundances of the major PC species is also briefly introduced.
    Keywords:  Lipidomic analyses; Muscular dystrophy; Phosphatidylcholine; Phospholipid compositions; Skeletal muscle
    DOI:  https://doi.org/10.1007/978-1-0716-4738-7_5